RNA fusion quant

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Snakemake workflow for RNA analysis of gene fusions and quantification of transcript expression.

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run on your local machine:

1. set up and configure units.tsv in config/ folder
2. add your genome & annotation of choice to the resources/ folder
3. identify the run folder (where the sequencer saved your run data)
4. do a dry-run and check if the right jobs are to be run

snakemake -npr --config runID="20230125_RNASeq"

5. run the job locally (choose the correct runID - this can be found in the SampleSheet.csv)

time snakemake -j48 --config runID="20230125_RNASeq"

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conda/mamba and other dependencies

create environment from yaml file (in envs/):

# create the environment (note that conda & mamba have to be installed for this to work):

mamba env create -f envs/s6.yaml

# with this, you can activate the environment with all [dependencies](https://github.com/schimar/rna_fusion_quant/blob/main/workflow/envs/s7.yaml):
conda activate smk6


# if you've added new software to install to the conda environment, then you can update:
mamba env update -f envs/s7.yaml

with SLURM, submit the job:

sbatch code/clusterSnakemake.sh

Deprecated (or rather: not used here): submit on PBS

qsub code/clusterSnakemake.pbs